Hi there, normalityrelief,
The synthy score is just a measure of what percentage of your photos Photosynth was able to match to each other, or to quote Nathan Wilfert, °In geek speak: it’s the probability that one can navigate between two photos selected at random, without replacement.°.
So, in answer to your question of why you are getting lower scores even as you add more groups of photos, the answer is simply that something about the different groups of photos is keeping Photosynth from matching them all together in the same cluster of photos. You should be able to see this when you view the different synths in 2D View (also called Grid Mode).
As you add more and more photos and the groups do not connect to each other, the percentage of photos that belong to the same point cloud is a lower and lower percentage.
The real question is what is so different about your batches of photos that they are not matching each other. Stage dressing? Lighting?